don't compare the HD fundamental with the Frequency Response.

the difference will be the high frequency accuracy. above the NF high frequency cutoff, the response will look different than if it were measured in the FF. the PDF should explain the details better than I can off the top of my head.

for FR, unless you have an anechoic chamber you are pretty much forced to merge NF/FF together. the point at which you do this will depend on both the NF high frequency cutoff and the point of first reflection in the farfield. the latter is typically 3ms for most people because this is where floor bounce occurs for most DIY'r type measurement setups.

I went through the trouble of building a HUGE baffle (10ft x 8ft) and treating a room so I could get the first reflection out to 10ms. in the end, it didn't really matter because the NF/FF merge took care of the issues I would otherwise have had to 'gate' out.

read through the PDF, though. it really does a great job of providing an intro into measuring speakers (which is TOTALLY different than just RTA'ing a system).